FEAT Accumulator for transfer learning

MannLabs / alphadia

modular & open DIA search

https://alphadia.readthedocs.io

Apache License 2.0

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FEAT Accumulator for transfer learning #106

Closed mo-sameh closed 5 months ago

mo-sameh commented 6 months ago

Introduced a method for constructing a TransferLib, used for fine-tuning purposes, using the output from a search. Additionally, added and used a linear accumulation strategy to mitigate memory constraints when aggregating data from a substantial number of experiments.

mo-sameh commented 5 months ago

@GeorgWa @mschwoer it should be ready to merge now.

mschwoer commented 5 months ago

@mo-same from my side it's alright to merge (otherwise I wouldn't have given approval ;-))

GeorgWa commented 5 months ago

Somehow it's not a yet requirement that tests are passing 🤔😄 I will take a look at the failing test @mo-sameh as this is due to using the same mock df for the outputtransform. 👍🏻

GeorgWa commented 5 months ago

Pinging @ammarcsj as this was somewhat directLFQ related:

The issue was that mock_fragment_df was broken and created dataframes containing the same fragment multiple times.

This lead to a dataframe which had duplicates in the quant_id which was (rightfully) not expected by directLFQ and resulted in a strange error when calling lfqnorm.NormalizationManagerSamplesOnSelectedProteins().